high performance computing on graphics processing units: hgpu.org

Applications

hgpu.org » Applications » Chemistry

Parallelization of tau-leap coarse-grained Monte Carlo simulations on GPUs

Lifan Xu, Michela Taufer, Stuart Collins, Dionisios G. Vlachos

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Tags: Chemistry, CUDA, Data parallelism, GPU cluster, Monte Carlo simulation, nVidia, Physics, Tesla S1070

June 9, 2011 by hgpu

Accelerating All-Atom Normal Mode Analysis with Graphics Processing Unit

Li Liu, Xiaofeng Liu, Jiayu Gong, Hualiang Jiang, Honglin Li

Tags: Biology, Chemistry, CUDA, Macromolecule, Molecular dynamics, nVidia, Pharmaceuticals

June 2, 2011 by hgpu

Accelerating Two Algorithms for Large-Scale Compound Selection on GPUs

Quan Liao, Jibo Wang, Ian A. Watson

Tags: Algorithms, Chemistry, Molecular simulation, nVidia

May 24, 2011 by hgpu

Acceleration of the GAMESS-UK electronic structure package on graphical processing units

Karl A. Wilkinson, Paul Sherwood, Martyn F. Guest, Kevin J. Naidoo

Tags: Chemistry, Fortran, Molecular dynamics, Molecular modeling, nVidia

May 21, 2011 by hgpu

GPU-based triangulation of the van der Waals surface

S. Dias, A. Gomes

Tags: Biology, Chemistry, Molecular modeling, Molecular surface

May 14, 2011 by hgpu

Fast Parallel Tandem Mass Spectral Library Searching Using GPU Hardware Acceleration

Lydia A. Baumgardner, Avinash K. Shanmugam, Henry Lam, Jimmy K. Eng, Daniel B. Martin

Tags: Biology, Chemistry, CUDA, nVidia, Search, Spectrometry

May 10, 2011 by hgpu

Efficient Parallelization of the Stochastic Simulation Algorithm for Chemically Reacting Systems On the Graphics Processing Unit

Hong Li, Linda Petzold

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Tags: Biology, Chemistry, CUDA, nVidia, nVidia GeForce 8800 GTX, Stochastic simulation

May 10, 2011 by hgpu

Improving numerical reproducibility and stability in large-scale numerical simulations on GPUs

Michela Taufer, Omar Padron, Philip Saponaro, Sandeep Patel

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Tags: Chemistry, CUDA, Floating point error, Molecular dynamics, nVidia, Tesla S1070

April 25, 2011 by hgpu

GPU-Based Implementations of the Noniterative Regularized-CCSD(T) Corrections: Applications to Strongly Correlated Systems

Wenjing Ma, Sriram Krishnamoorthy, Oreste Villa, Karol Kowalski

Tags: Chemistry, Molecular modeling

April 15, 2011 by hgpu

GPGPU supported cooperative acceleration in molecular dynamics

Gang Chen, Guobo Li, Songwen Pei, Baifeng Wu

Tags: ATI, Brook, Chemistry, Molecular dynamics

April 5, 2011 by hgpu

Accelerating Molecular Docking Calculations Using Graphics Processing Units

Oliver Korb, Thomas Stutzle, Thomas E. Exner

Tags: Algorithms, Chemistry, Molecular modeling

March 28, 2011 by hgpu

GPU Acceleration of High-Speed Collision Molecular Dynamics Simulation

Canqun Yang, Qiang Wu, Juan Chen, Zhen Ge

Tags: Chemistry, CUDA, Molecular dynamics, nVidia, Tesla C870

March 25, 2011 by hgpu

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

Profile Util library: A quick and easy way to get MPI, OpenMP and GPU runtime information

MaC: Mamba CPU performance predictor

MambaCPU: Enhanced Correlation Mining with State Space Models for CPU Performance Prediction

Mixed-precision finite element kernels

Mixed-precision finite element kernels and assembly: Rounding error analysis and hardware acceleration

SHMT: The Simultaneous and Heterogenous Multithreading project

General-Purpose Computing on Tensor Processors

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

Online Energy Optimization in GPUs: A Multi-Armed Bandit Approach

See all packages

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high performance computing on graphics processing units: hgpu.org

Applications

Parallelization of tau-leap coarse-grained Monte Carlo simulations on GPUs

Accelerating All-Atom Normal Mode Analysis with Graphics Processing Unit

Accelerating Two Algorithms for Large-Scale Compound Selection on GPUs

Acceleration of the GAMESS-UK electronic structure package on graphical processing units

GPU-based triangulation of the van der Waals surface

Fast Parallel Tandem Mass Spectral Library Searching Using GPU Hardware Acceleration

Efficient Parallelization of the Stochastic Simulation Algorithm for Chemically Reacting Systems On the Graphics Processing Unit

Improving numerical reproducibility and stability in large-scale numerical simulations on GPUs

GPU-Based Implementations of the Noniterative Regularized-CCSD(T) Corrections: Applications to Strongly Correlated Systems

GPGPU supported cooperative acceleration in molecular dynamics

Accelerating Molecular Docking Calculations Using Graphics Processing Units

GPU Acceleration of High-Speed Collision Molecular Dynamics Simulation

Recent source codes

Kokkidio: Kokkos+Eigen - write fast, readable multi-platform code

LLaMA-Inference-Bench

MATAR

Over-synchronization in GPU Programs

profile_util: simple C++ library to report memory, timing, thread affinity

MaC: Mamba CPU performance predictor

Mixed-precision finite element kernels

SHMT: The Simultaneous and Heterogenous Multithreading project

Superpipeline: A Universal Approach for Reducing GPU Memory Usage in Large Models

EnergyUCB-Bandit

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